Geany is an IDE/editor, so converting large numbers of files encodings is not considered a common use-case. So the efficiency of the UI for that purpose has not been optimised.
To convert lots of files you would be better off using `iconv` on the command line or possibly in a script.
So its unlikley that any complex changes to the UI or a keybinding GUI in this area will happen unless somebody contributes it.
Its possible the menu order could be sorted, but again somebody has to do it.